Enemies have a visible awareness cone based on line of sight. Next to white that shows the reach of their sight, there is a yellow state where guards investigate and a red state where they alert others and attack. Jun has a large amount of abilities to wield stealth. She can take cover in alcoves and assassinate from there and assassinate from ledges. Guards spot bodies so these need to be hidden in alcoves or green chests. Enemies can be distracted with a dog whistle, triggering a yellow awareness state and the player can determine the position, reach and strength. There are sometimes dogs that need to be avoided as the barking will draw guards. The game has minor puzzle elements to progress with levers and objects that can be interacted with. In complex situations with multiple guards their patrol paths need to be taken into account. The game brings over the eagle vision feature from the main series where paths become visible through bright colours.
Jun can assassinate with a hidden shoe blade, but she can also engage in regular combat with a sword using mechanics to perform two types of attacks, block and roll over. It is also possible to block backwards and dodge bullets. Various gadgets are unlocked gradually, such as daggers to trigger wind chimes or attack from a distance, noise darts, firecrackers that stun, a grappling hook etc. Additional abilities such as dashing between hiding places become available gradually. After each level a number of upgrades can be unlocked. There are also secondary objectives and optional hidden collectibles. Just like the main games it is presented as an Animus simulation so Jun cannot die, but desynchronizes. Also carried over from the main games is the Animus database where descriptions about people and locations are stored as they are encountered. Next to the normal mode a plus and plus hard mode can be unlocked. Existing abilities and upgrades are carried over, but in plus hard for instance Jun has only a single health bar and enemies react faster.